Getting Started with NC State's Intel/IBM Linux Cluster at MCNC

• Sam System Configuration

  There are approximately 1000 dual Xeon nodes. Each node has two Intel Irwindale Xeon processors, four GB of memory, and a 40 GB disk. There are nodes available for interactive code development. The compute nodes are managed by the LSF queuing system and are not for access except through LSF (accounts directly accessing a compute node are subject to immediate termination). Compute nodes are interconnected with gigabit Ethernet.

  Logins for the sam cluster are handled by the interactive nodes.

• Logging onto the cluster SSH access is supported to the interactive nodes which are reached using hostname loginhpc.dcs.mcnc.org Authentication uses Unity IDs and passwords.
  Free SSH clients are available from various sources. Links to some commonly used versions are included here:
  • Windows
  • Unix, Linux

• File Systems AFS files are not available from the cluster. Users have a home directory that is shared by all the sam cluster nodes. This is not the same home directory as is used on the BladeCenter Linux cluster (henry2).

  The /usr/local file system is also shared by all nodes. Each node currently has its own local /scratch file system that is available to all users and a shared scratch parallel file system /gpfs_share (this is also not the same file system available on henry2 cluster).

  Currently no backups are being performed on any file system mounted on the sam cluster!

• Compiling

  There is currently one supported compiler, Portland Group, available for use on the sam cluster. While GNU compilers are installed their use is strongly discouraged and is not supported.

  • Portland Group Compilers To use the 64-bit Portland Group compilers it is necessary to properly configure some environment variables and paths. For csh/tcsh shell users a shortcut is available by using an alias which has been created - add.

    add pgi
    

    Will configure the environment to use the Portland Group compilers.

    Once these have been set the Portland Group compilers may be invoked with the pgcc, pgcpp, pgf77, pgf90, and pghpf commands for the C, C++, Fortran77, Fortran90, and High Performance Fortran compilers respectively.

    Parallel programs compiled with the Portland Group compilers should be linked with the Portland Group MPICH libaries.

    Having added the pgi envirnomment by

    add pgi
    

    the following command line line would compile an MPI Fortran 90 code with a high level of optimization:

    pgf90 -o exec -fastsse -Mmpi exec.f 
    

• Running Jobs Access to the compute nodes is managed by LSF. All tasks for the compute nodes should be submitted to LSF.

  The following steps are used to submit jobs to LSF:

  • Create a script file containing the commands to be executed for your job:

    #BSUB -o standard_output
    #BSUB -e standard_error
    
    cp input /share/myuserid/input
    cd /share/myuserid
    ./job.exe < input
    cp output /home/myuserid
    
    

  • Use the bsub command to submit the script to the batch system. In the following example two hours of run time are requested:

    bsub -W 2:00 < script.csh
    

  • The bjobs command can be used to monitor the progress of a job
  • The -e and -o options specify the files for standard error and standard output respectively. If these are not specified the standard output and standard error will be sent by email to the account submitting the job.
  • The bpeek command can be used to view standard output and standard error for a running job.
  • The bkill command can be used to remove a job from LSF (regardless of current job status).

  For parallel jobs it is necessary for LSF to interface with the mpirun command to pass host and process information. To enable the LSF/MPI interface a script mpirun.lsf has been provided in the LSF bin directory. The following batch script will run a parallel job, note that the number of MPI tasks will match the number of processors requested from LSF.

  #BSUB -n 4
  #BSUB -W 60
  #BSUB -J job
  #BSUB -o standard_output.%J
  #BSUB -e standard_error.%J
  #BSUB -a mpichp4
  
  mpiexec ./parjob.exe
  

  Alternatively, replace the "mpiexec" line by

  mpirun.lsf /whateverthefullpathis/parjob.exe
  

  The #BSUB lines in the script pass options to the LSF bsub command. The -n option specifies the number of processors, -W specifies the run limit in minutes, -J provides a meaningful name for the job, -o specifies a file to hold standard output, -e specifies a file to hold standard error output, and -a mpichp4 identifies to LSF that the job will use MPI and the type of MPI being used.

  The script can be submitted to LSF for execution using the command:

  bsub < script.csh
  

  LSF writes some intermediate files in the user's home directory while the job is running. If the disk quota has been exceeded, then the batch job will fail, often without any meaningful error message.

Last modified: April 19 2013 11:37:35.